The FONA³ programme structure includes three systems of high relevance for sustainable development, implemented in the form of flagship initiatives: Green Economy, Future City and Energy Transition. FONA³ is focusing a large part of the funded sustainability research on the implementation of research results into concrete technical and social innovations. A central aspect of this approach is supporting companies in taking up new research findings and applying them as quickly as possible for innovative products, processes and services.

In addition to the three flagship initiatives mentioned above, the research areas of FONA2 are still relevant, and their long-term achievement can only succeed if, in addition to already applicable solutions, the fields of knowledge are advanced and basic knowledge is extended in the research fields.  Following on from FONA2, FONA³ focuses on four overlapping areas of preventive research: Securing and improving quality of life and competitiveness, conserving resources and using them intelligently, protecting the common goods of climate, biodiversity, land and ocean and education and research: together for sustainable development. Research and education are closely interlinked in this framework program, because a sustainable society needs not only technological but also societal innovations. FONA³ is continuing to use proven elements, such as the joint research funding tool and the high degree of interdisciplinarity and transdisciplinarity, in an advanced form.